Mayflower: A Voyage to War by Nathaniel Philbrick 461pp, Harper Press, £20

All nations produce myths of their unique origins, and these are usually comforting. Along these lines, Americans celebrate Thanksgiving in late November. It's a cosy holiday, with family gathered, a fat turkey on the table and pumpkin pie waiting in the wings. It's a time to give thanks for family and friends, and - subliminally, perhaps - to think about the Pilgrims and how friendly Indians helped them survive a difficult year. Every American learns some version of the mythic story: the brave and resilient Pilgrims arrived in Plymouth, Massachusetts, in 1620 on the Mayflower. They were, as Nathaniel Philbrick notes in his marvellous new book, a band of "dissidents who had come to define themselves in opposition to an established authority." In search of religious freedom, they undertook a harrowing passage across stormy seas, and many died along the way. Those who didn't may have wished they had, as starvation and disease lay ahead, thinning their ranks by half. A further shipload arrived in 1621. This replenished group broke bread with the local Pokanoket tribe, whose "sachem" (chief) was the legendary Massasoit.

That's where the story usually stops. As Philbrick retells it in Mayflower, there was more going on than usually meets the eye. Indeed, that first Thanksgiving is hardly the end of the story. Half a century of carefully brokered peace followed, and this was no mean feat. Both sides had inspired leadership. Massasoit was clever and politically adroit, a fitting counterpart to Governor William Bradford, whose account of the Pilgrims' adventures in Of Plymouth Plantation remains a key historical document.

Philbrick is well placed to tell this story. He won a National Book Award for In the Heart of the Sea (2000), a vivid account of the true story behind Melville's Moby-Dick. He has written books on sailing and maritime exploration. He has also written with deep sympathy about the Native American legacy of Nantucket Island, where he lives. He brings all of this interest and information to bear in Mayflower, which is popular history at its best.

Bradford devoted only a few paragraphs to the Atlantic crossing, but Philbrick fills in the historical blanks with his knowledge of seagoing in the early 17th century. It was not easy to undertake such a voyage in a ship like the Mayflower, "a typical merchant vessel of her day: square-rigged and beak bowed, with high, castlelike superstructures fore and aft that protected her cargo and crew in the worst weather, but made beating against the wind a painfully inefficient endeavour."

The bedraggled Pilgrims arrived in an unfamiliar land populated by an indigenous people who had recently suffered ravages of their own. A mysterious illness - perhaps bubonic plague brought by Europeans on fishing expeditions - had wiped out a huge portion of the native population. The relations that followed between these wildly different cultures were undertaken with caution and due sympathy on both sides. It's hardly a simple tale of oppressive colonists. Nor could one say that the Indians were guileless or without their own resources.

The colonists soon quarrelled about how to deal with the Pokanoket, who in turn took various positions on the colonists and other Native American tribes. "Not only had the Pilgrims proved unexpectedly violent and vindictive," writes Philbrick, "but Massasoit had betrayed his former confederates. By siding with the Pilgrims against the Indians of Massachusetts and Cape Cod, the Pokanoket sachem had initiated a new and terrifying era in New England. It was no longer a question of Indian versus English; it was now possible for alliances and feuds to reach across racial lines in a confusing amalgam of cultures."

Peace requires effort and compromise, as William Bradford and Massasoit both understood. Their wisdom did not survive their passing. Vengeful rivalries and betrayals led to what was called King Philip's War, waged by Matacomet (also called Philip), the son of Massasoit. Hostilities erupted in 1675, when the rigid Josiah Winslow was governor of the Plymouth Colony. The colonists, as Philbrick argues, began to demonise the Indians as agents of evil. "This meant that there was nothing to be achieved through diplomacy."

With reinforcements from the Massachusetts Bay Colony, and led by Benjamin Church - a wily and fascinating figure - the war raged and expanded throughout New England. It was a complex affair, with Church welcoming "all potentially neutral Indians" as allies. The Plymouth Colony lost 8% of its male population - making it the most lethal war in American history (even the Civil War had a casualty rate of only 4% or 5%). This was nothing compared to the Indian side: "Overall, the Native American population of southern New England had sustained a loss of somewhere between 60 and 80 per cent." What had begun as a squabble between Philip and the tiny Plymouth colony soon metastasised into regional war. The consequences were far-reaching, leading ultimately to the near-destruction of the Native American population. As Philbrick wisely observes, "unbridled arrogance and fear only feed the flames of violence". But he refuses to take a lopsided position with regard to the Pilgrims, and sensibly asks readers to take a sympathetic backward look at these intrepid settlers, who, under the inspired leadership of Bradford and others, "maintained more than half a century of peace with their Native neighbours" before all hell broke loose.

· Jay Parini 's The Art of Subtraction: New and Selected Poems is published by George Braziller